| Variant ID: vg1022632151 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 22632151 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 107. )
GGCGGCTCCTCCTCCGTCTCCGTCTCCGTCTCCGGCGCCGCCCTCTTCTGCACGACGACGACGGGACTTGCTGTTCGGTTGGCATCGGCTAACAAGACTG[C/A]
GGAGAACGCTTGTGCTTCCGCAATCTCCGCCTCGGCCGTCGCGGCGTGCTTCTGCAGCGCCTGCACGAGCTCCTCCTCGCCCGCAAAGAAGACGGCGGCG
CGCCGCCGTCTTCTTTGCGGGCGAGGAGGAGCTCGTGCAGGCGCTGCAGAAGCACGCCGCGACGGCCGAGGCGGAGATTGCGGAAGCACAAGCGTTCTCC[G/T]
CAGTCTTGTTAGCCGATGCCAACCGAACAGCAAGTCCCGTCGTCGTCGTGCAGAAGAGGGCGGCGCCGGAGACGGAGACGGAGACGGAGGAGGAGCCGCC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 46.10% | 1.90% | 0.85% | 51.21% | NA |
| All Indica | 2759 | 12.90% | 3.20% | 1.41% | 82.46% | NA |
| All Japonica | 1512 | 96.20% | 0.00% | 0.00% | 3.77% | NA |
| Aus | 269 | 78.40% | 0.00% | 0.37% | 21.19% | NA |
| Indica I | 595 | 9.40% | 0.30% | 0.67% | 89.58% | NA |
| Indica II | 465 | 17.00% | 14.00% | 2.15% | 66.88% | NA |
| Indica III | 913 | 7.60% | 0.00% | 1.20% | 91.24% | NA |
| Indica Intermediate | 786 | 19.50% | 2.70% | 1.78% | 76.08% | NA |
| Temperate Japonica | 767 | 99.50% | 0.00% | 0.00% | 0.52% | NA |
| Tropical Japonica | 504 | 89.90% | 0.00% | 0.00% | 10.12% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 66.70% | 1.10% | 0.00% | 32.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1022632151 | C -> A | LOC_Os10g42072.1 | missense_variant ; p.Ala230Ser; MODERATE | nonsynonymous_codon ; A230S | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | unknown | unknown | TOLERATED | 0.06 |
| vg1022632151 | C -> DEL | LOC_Os10g42072.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |